With the pencil very sharp I use one like this
the pointed metal end rides in the fret slot one each side of where the dot will go. Actual center will be between those two lines. I use this same tool to find center the long way as well running it along the side edge. Most hardware stores of any size carry these compasses. They only cost a couple of bucks.The only time you need to measure is when setting the distance from the outside you want to set double dots. On a board that is already tapered, set your compass to this amount and run along the outside edge. It is best to then set a fence of some sort for drilling the double dots that will keep this distance from outer edge the same. To drill I use a brad point bit. I hold my work in a cheap cross vise I got from harbor freight. This makes it easy.
You really shouldn't be doing a lot of measuring and marking. Measuring and marking will introduce error.
